Contacts of the helix formed by residues 323 - 333 (chain A) in PDB entry 3ENM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A ILE* 4.0 9.5 - - - +
322A THR* 1.3 74.9 - - - +
324A VAL* 1.3 58.5 + - - +
325A ALA* 3.4 6.4 + - - +
326A SER* 2.5 46.2 + - - -
327A PHE* 4.1 4.9 + - - +
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 4.0 31.0 - - + -
157A LYS* 3.7 34.5 - - + -
187A ILE* 4.2 7.4 - - + -
191A GLY* 3.4 32.1 - - - +
193A VAL* 5.0 4.0 - - + -
322A THR* 3.1 10.9 + - + +
323A ASP* 1.3 72.3 - - - +
325A ALA* 1.3 66.9 + - - +
327A PHE* 3.0 14.9 + - - +
328A VAL* 3.0 28.1 + - + +
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ALA 3.3 21.5 - - - +
190A LEU* 3.7 16.4 - - - +
191A GLY* 3.8 7.8 - - - -
323A ASP* 3.4 4.9 + - - +
324A VAL* 1.3 78.4 - - - +
326A SER* 1.3 58.2 + - - +
328A VAL* 3.2 3.4 + - - +
329A LYS* 2.9 46.5 + - - +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A ASP* 2.5 36.9 + - - -
325A ALA* 1.3 77.7 - - - +
327A PHE* 1.3 60.9 + - - +
329A LYS* 3.4 9.2 + - - +
330A LEU* 2.5 43.3 + - - +
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Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PHE* 3.8 24.2 - + - -
143A VAL* 4.4 4.5 - - + -
148A GLN* 4.2 12.3 - - + -
149A THR 3.3 24.9 - - - -
150A ILE* 4.4 5.8 - - + -
151A PRO* 3.6 24.0 - - + -
154A ILE* 3.4 34.8 - - + -
323A ASP 4.1 2.4 + - - +
324A VAL 3.0 3.3 + - - +
326A SER* 1.3 80.3 - - - +
328A VAL* 1.3 60.1 + - + +
330A LEU* 3.6 6.9 - - + +
331A ILE* 3.0 65.1 + - + +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PHE* 4.1 19.5 - - + -
154A ILE* 5.6 0.4 - - + -
187A ILE* 3.6 33.4 - - + -
188A ASN 3.9 24.0 - - - +
189A ALA* 4.4 4.5 - - + -
324A VAL* 3.0 22.7 + - + +
325A ALA 3.7 6.3 - - - +
326A SER 3.2 0.2 - - - -
327A PHE* 1.3 78.3 - - + +
329A LYS* 1.3 59.5 + - - +
331A ILE 3.2 1.0 + - - -
332A LEU* 2.8 52.2 + - + +
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Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ALA* 3.9 33.6 + - + +
325A ALA* 2.9 32.9 + - - +
326A SER* 4.0 9.2 - - - +
328A VAL* 1.3 75.9 - - - +
330A LEU* 1.3 62.1 + - + +
332A LEU* 4.3 3.8 - - - +
333A ALA* 3.0 37.3 + - + +
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LYS* 4.0 11.6 + - - +
326A SER* 2.5 48.0 + - - +
327A PHE* 3.6 8.7 - - + +
329A LYS* 1.3 84.3 - - + +
331A ILE* 1.3 64.2 + - + +
333A ALA* 3.7 8.3 + - - +
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Residues in contact with ILE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PHE* 3.7 21.3 - - + -
142A GLN* 3.1 41.3 - - + +
143A VAL* 3.9 23.1 - - + +
146A LYS* 3.6 17.4 - - + +
148A GLN* 3.9 20.0 - - + -
327A PHE* 3.0 57.1 + - + +
328A VAL 3.8 2.9 - - - +
330A LEU* 1.3 77.7 - - + +
332A LEU* 1.3 61.7 + - + +
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ASP* 3.7 31.6 - - + +
134A THR* 3.8 23.6 - - + -
139A PHE* 4.1 18.4 - - + -
142A GLN* 4.4 14.3 - - + +
189A ALA* 6.1 0.4 - - + -
328A VAL* 2.8 35.1 + - + +
329A LYS* 4.3 3.6 - - - +
331A ILE* 1.3 85.2 - - - +
333A ALA* 1.3 58.4 + - + +
58C GLU* 3.3 25.0 - - + +
59C LEU 4.5 9.4 - - - +
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LYS* 3.2 18.3 + - - -
329A LYS* 3.0 20.4 + - + +
330A LEU* 3.7 4.8 + - - +
331A ILE 3.4 2.0 - - - -
332A LEU* 1.3 78.5 - - + +
58C GLU* 3.2 23.8 - - - +
59C LEU 5.8 0.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il